... unlike fighters, you can refit them. ...

FYI - You can actually refit fighters in a shipyard, same as any other vessel.

In the end it really is not super important what ships and size of them you use. Bigger is more efficient per tonnage and smaller provide much better stealth capabilities, both thermal and active cross section reflections. The point is rather how you use them.

If you are using missiles as your main form of attacking you always want to be able to fire without them able to fire back... there are basically two ways to do this. Either you use a stealthy platform or you use extremely long range missiles. Both have advantages and disadvantages.

The thing is... under no circumstance do you want to fight on equal terms. This is why stealth or range is so important. In addition to this so is reconnaissance and strategic planning. If they bring 50kt you bring 500kt fleet. The thing is... building a fleet for attacking is so much more expensive than one meant for defence. You don't only need the ships with more engines and fuel, you also need logistics, bases and defences.

What does this have to do with size of strike craft?!?

It does... when you do decide to attack you have to bring something decisive. If this is a fleet ten times stronger or more of a smaller surgical tool is a strategic choice. If you can fly a smaller craft relatively close and fire their missiles without being retaliated you can more or less attack an enemy with impunity and they will not even know where your fleet is. If you attack with your fighters and you somehow misjudged them you might loose some crafts and can withdraw. If you reveal your entire fleet you just put all eggs in one basket and you better not misjudged the situation.

The same thing goes for size of strike crafts... the bigger the craft the more likely it is the opponent will detect them so the longer they reach they must have in order not to be detected. What you gain in efficiency you loose in stealth.

When you then look at the industrial cost of building all these carriers, escorts, strike crafts etc..  you need to judge how you will be able to overmatch the opponent for as low a cost as possible. If you are stealthy you can probably use cheaper engine as speed will not be as important. This goes for both carrier and strike crafts, this reduce costs and increase efficiencies.

In my experience stealth is almost always better than brute force... it is cheaper and safer in the long run.

Now... the AI never adapt to your strategies... so against the AI you can just study their sensor types used and then figure a best size strike craft and what weaponry or missiles you want and you can defeat them quite easily. So... build your strategy around what you know and adapt that doctrine based on facts rather than some stipulated rules. If you are playing a game where there are more than one human run faction it get's complicated real fast but the principals are the same.

Andrew is correct.

To expound a bit (spoilers for NPR ship design hidden for those who enjoy the journey of discovery): NPR fleets usually have a set of sensors covering resolutions 1 (50-ton, anti-missile sensor), 5 (250-ton), 20 (1000-ton), and somewhere north of 100 (5000-ton, general-purpose). If you work through the sensor math, this usually means that FACs of ~1,000 tons will be detected at about 1.6x the range as 500-ton or smaller fighters. This means that against missile-based NPR fleets, fighters can get closer and thus need smaller MFCs/sensors, can use faster/stronger missiles with shorter range, and so on, compared to FACs. Of course, you can also abuse this knowledge to find the tonnage "sweet spots" (around 145 tons for fighters and 630 tons for FACs, incidentally)... the point is simply that playing around the limits of enemy sensor range with your parasite tonnage has a potentially significant effect on your ability to close in without detection and launch from an optimal position. This is one of many reasons why playing a multi-player-race game can be quite interesting, if every race has its own sensor doctrine then gathering intelligence about sensor types can be critical to aid in designing the right counter-force.

Against a beam-only enemy fleet, then it doesn't really matter and you can go nuts with tonnage efficiency.

No, its down to the sensor resolution and the size of each target, so a sensor resulution of 25,000 tons would spot a 25,000 ton ship at its rather long maximim range. while it would not spot 1000, 250 ton fighters until they were close enough for that sensor to spot , or they ran into it.
Unless a ship has a sensor tuned for fighters then they can probably avoid detection until they reach the detection range of the resolution 1 antimissile sensors

There are pros and cons either way. The main advantage of a FAC over a fighter is, as you state, better tonnage efficiency, even something as simple as having more weapons per fire control is helpful. This is also the advantage of a 500-ton fighter versus a 250-ton fighter, for example, so it is hardly unique. The advantage of the smaller fighter is that it is harder to detect for the enemy and therefore, at least in principle, safe from retaliation as it closes to weapons range, particularly for missile bombers.

There is also an advantage for large numbers of very small fighters which is that once your craft dies in one hit anyways, the more of them you have the more you can overwhelm the enemy BFCs with sheer numbers, which is one route for large swarms of beam fighters to beat larger fleets. Actually, this is the major reason to even use FACs instead of large ships, otherwise if tonnage efficiency was the sole determinant of combat ability the winning combination would be having as many zeroes as possible in the tonnage measurement.

To sum up, I think both approaches have something going for them and are strong when used correctly. It's all in the fleet doctrine and tactics. 

I tried it with slightly larger FAC;s slow and the carrier was intended to fight with them but each FAC carried a large spinal laser or similar weaponso I could effetively carrry multiple spinal lasers on one ship

I go far more extreme.  My latest carrier launched ships are 30ktons, going 20kkm at magneto plasma.

Yeah, having so-called 'fleet carriers' that carry proper ships instead of just strike crafts are something I'd like to do, but only in the super late game. For the rest of the game I think that FACs provide the most amount of available tonnage for your buck seeing as they don't need bridges and can be quickly churned out at shipyards.